Whispers Through Time
by BeagMacTire
Summary: Prompted by a Tumblr conversation about how awesome it would be if Jaime Murray became the next Doctor. The Doctor wakes up from in her twelfth regeneration to find there is something very different; No not ginger- she's a she. The Tardis throws them into the future, where the Doctor finds herself at the death bed of an unknown woman. Doctor who and Warehouse 13 aren't mine.
1. Chapter 1

**I realise I have too many fics on the go, but this one will not leave me alone; it has it's claws in me.**

**Prompted by a Tumblr conversation about how awesome it would be if Jaime Murray became the next Doctor. **

Opening her eyes, after shielding them from the blinding light, Clara looked to the form lying on the ground, "Doctor?"  
Shifting with a groan, the Doctor groaned, "God that was a rough one."  
Clara's eyes nearly popped out of her skull when she found herself face to face with an incredibly attractive, ebony haired woman. Looking around, the woman asked, "What's wrong?" She paused, "Wait... what's wrong? Have I got four eyes? Two noses?!" Panicking, the Doctor's hands desperately searched her face. Jumping to the Tardis console, she grabbed the mirror, "Bloody hell!" Standing up, her eyes were wide with shock, "Clara! I'm a woman!"  
Her companion nodded, equally shocked, "Yeah, I know!"  
Going back to the mirror, she muttered, "A woman, and still not ginger. I like this though." Pawing her own hair, she grinned, "It's so soft! Aces!" Bounding over, she grabbed Clara's hand, "See! Feel it!"  
"Doctor, I'm not going to... Jesus! You're right!"  
"I know!" When her voice reached a high girlish squeak of excitement, the Doctor jumped back with her hands covering her mouth, "Oh! New voice! Strange voice, not very deep…" She paused, "Oooh, though I do like it." Grinning, she winked at Clara, "It's just a little like crushed silk, and oh so foxy... No, not foxy, sexy... No I can't be sexy." She stroked the Tardis Console, "You're sexy I can't be." Frowning, she began muttering to herself, "So who can I be?"  
Clara shook her head, and offered, "The Doctor?"  
Spinning, she gave a light laugh, "Yes! I shall be the Doctor!" Pausing, she ran a hand through her hair in thought, "I'm going to need a new name. I can't very well going around calling myself John Smith can I?... I know!" Darting off, Clara was left standing at the console. Looking up she sighed, "He... she's still as mad as ever; I suppose that hasn't changed."  
The Tardis seemed to hum in agreement as the Doctor reappeared with a handful of books, "Jules Verne? Nope!" She muttered the name of each author followed by a swift, "Nope!" And tossed the book carefully into a surprisingly neat pile on the Tardis console.  
Weighing a copy of the Time Machine in her hands, the Doctor paused.  
It was at that moment, Clara's phone went off. With a grin, she held it up, "It's my friend Helena, I'll be right back."  
" Hmm." Brushing her fingers over the leather tome, she muttered thoughtfully, "Helena."

Hopping around the console, flicking switches here there and everywhere, the Doctor asked, "So then! Where to? Forward, backwards, sideways?"  
Leaning on the console, Clara asked, "So, what does this mean now? You're a woman?"  
Turning, the Doctor nodded nonchalantly, "Oh yes darling, all woman."  
"But you were a man."  
With a sigh, the Doctor flipped a switch bringing the Tardis to a shuddering halt, "With each regeneration comes something different. We are like different people, but on the same token; we are the same people. We share the same memories, same experiences. But we each have our own personalities and quirks; but there are basic elements that remain" Taking a step towards the young woman, she touched her arm comfortingly, "I'm still the Doctor." Tilting her head, she asked, "Clara? Are you alright?"  
"Yeah, it's just going to take some getting used to; that's all."  
"Okay. Just let me know if you want me to take you home or..."  
"No!" The young woman yelled suddenly, "No! I don't want to go home; I couldn't care less if you were a twelve armed rhino woman with a tail; I'd still want to travel with you. This... it's become my life. You can't kick me off now just because you've turned into a goddess over night."  
Grinning, the Doctor saluted her, "Aye Aye." Turning to the console, she grabbed the switch, "Righty ho then!" Slamming it down, as per usual; the Tardis decided to go beserk.

Losing her grip on the console, the Doctor fell back against the railings with a wince as the Tardis landed roughly. Pulling herself up, she frowned, "What was that about?" Stroking the console, she asked, "Hey, what's wrong?"  
The doors opened of their own fruition, looking to the exit, she nodded, "Okay. I'm going."  
Untangling herself from the mass of wires she had fallen into, Clara made to follow; but as soon as the Doctor went through the doors slammed shut.  
With an indignant huff, she banged on the door, "Really?! I thought we had sorted this!"

Cautiously the Doctor padded through what appeared to be a hospital. Her steps were measured and her eyes scanned for any danger.  
A nurse spotted her, "You came." The young woman, eyes bright, but weighted with the sorrow of one who aids the dying. "She said you would but... All of them say that." A genuinely relieved smile spread over the nurse's features, "She's through here; I'm afraid she doesn't have long."  
Taking the Nurse's hand, she allowed herself to be lead through the hospital into a private room.  
In the bed lay a woman no older than her early sixties. Long curly brown hair was streaked with grey, her features though worn with age, indicated she was and still was an incredibly beautiful woman. The Nurse urged the Doctor in, her voice lowered to a solemn whisper, "I think she's been waiting for you. Once the cancer spread, there wasn't anything we could do for her."  
"I..." She took a deep breath, the air had suddenly filled with the smell of apples, "I smell apples."  
"Helena?" The woman in the bed stirred, her voice raw and weak, "Helena? Is it you?"  
Taking a step back, the Doctor didn't know what to do. The Nurse, seeing her panic whispered in her ear, "Just let her know you're here."  
Uncomfortable, the Time Lord made her way to the bedside and took the woman's hand, careful to avoid the IV, "I'm here."  
With barely the strength to tighten her grip, the woman tried to squeeze her hand, "I knew you'd come. That somehow you'd find me." Her voice was fading, and the Doctor had to lean in to hear it, "You would be so proud of Ruby. She's a member of the secret service now; and she remembers everything you taught her." Pausing, the woman indicated she wanted the Doctor to come closer, "I know you aren't my Helena; but you will be. Just know that I never stopped loving you Helena Wells." Pressing her lips to the Doctor's cheek, she released one final whisper, "I smell apples."  
She didn't know why, or how, but her eyes were filled with tears. Standing, she inclined her head towards the nurse. Outside the private room, she covered her mouth with her hand as an unexplainable cry of anguish wanted to break free; swallowing it, she stared wide eyed at the ceiling. Who was this woman; and why were both her hearts breaking like glass?

**Worth Continuing?**


	2. Chapter 2

**Hey! It's a day later than I had hoped to post it, but hey ho! Give me a few days for the next one; in theory I should be working... My bad! **

**I was blown away by the amazing response, thank you all so much for your amazing reviews, your follows and favourites. I hope I do you proud.**

There was something unreadable and wild in the Doctor's eyes as she charged back into the Tardis.  
Clara leapt to her feet, she took one look at the other woman's expression and her stomach dropped, "Doctor? What happened? Are you alright..."  
Storming up to the console, she took one breath before settling her features. Turning with a smile, she nodded, "Yes, yes, everything is fine. Now." Placing her hand on the controls once more, she blinked away the last remnants of her rebellious tears, "Righty ho then! Let's go to... Ancient Greece!"

As the doctor leapt for the Tardis door, she felt something snag her coat and propel her the rest of the way towards the Tardis. Looking down at the brown trench coat, she realised it was pinned to the Tardis door by a spear. "Bollocks!" Seeing the charging soldiers, she quickly grabbed the sonic screwdriver from the pocket, jumped out of the coat and into the Tardis; slamming the door with a loud bang. Clara hung from the railings, gulping in air like crazy, "What just happened back there?!"  
The Doctor looked back to the doors indignantly as she began to fiddle with the console, "I have no idea! They didn't get this offended the last time I... oh! Right, female; I really must remember that!" A loud bang came at the door, spinning Clara yelled, "Get us out of here!"  
"Working on it darling!" A large explosion of sparks rained down on them from the central control panel. Jumping out of the way, both the Doctor and Clara found themselves being thrown over the railings to the floor below.  
With a groan, the Doctor sat up. her eyes widened, as she yelled, "Ah!" Popping up, the she swung herself onto the floor of the central platform. Stroking the controls with loving care, she whispered, "Are you alright?"  
Clara stumbled to her feet, "What?!"  
Frowning, the Doctor gave an exasperated sigh, "I wasn't talking to you." Almost skipping around the consol, she ran her fingers over a few burn marks, "Oh I am sorry, I know you hate it when I put you on random, but we had to get out quickly." Pausing, she straightened, "Actually, where are we?"  
Rubbing the fast growing lump on her head, Clara grumbled, "You mean, you don't know where we are? Well there's a surprise!"  
"Really Clara, sarcasm is not befitting a young lady such as yourself."  
Putting her hands on her hips, Clara huffed, "You're a hell of a lot more sarky than you were before."  
"Shh!"  
Staring incredulously, Clara began agiain, "Excuse..."  
"Shh!" Moving carefully around the central console, the Doctor put her ear to the controls. Her eyes were puzzled a moment before she released a hiss of, "Bollocks." Stepping back she ran a frustrated hand though her head, "Oh bollocks, bollocks, Bollocks!"  
"Doctor, what's wrong?"  
Looking up, the ebony haired woman had begun to pace, "Bollocks... I should have known they wouldn't give up that easily. They know I regenerate; killing me once won't be enough."  
Clara rushed towards the Time Lord, "The Aubertides? They're still coming for you?!"  
Nodding, the Doctor gave a frustrated growl, "Yes, they've put a tracking device on the Tardis. I can't get rid of it." Holding her hair she huffed, "Yeah, they're an off shoot of a hunting party called the Family of Blood. Their matriarch has a thing against me."  
Clara nodded, "Yeah, you never explained why."  
"I trapped her behind mirrors for a millenia; and placed her family in eternal prisons." Flicking another switch she muttered, "I can't believe I'm doing this again."  
As the Doctor ran into one of the back rooms, Clara followed close behind, "Doing what?"  
Pulling a strange looking headset from the ceiling, the Doctor winced at it, "Chameleon Arch." Her face twisted, "It's going to make me human." Pausing, she considered a moment, "We do however, have one main advantage."  
Clara's mind was working overtime, and her responses came as if she was on autopilot, "And what's that then?"  
Grinning, the Doctor gestured to herself, "They are looking for someone distinctly more male than myself." Pushing the fob watch into the Arch, she began to hurriedly explain, "The Chameleon Arch will store my Time Lord Essence in this fob watch. I'll be automatically integrated and given a back-story; you'll have to find a way to fit in." Unhooking a ring from the Chameleon arch, the Doctor pushed it into Cara's palm, "This will help you locate the family." The ring had a circular stone set in it, "When the stone is any shade of red the family are in the same world as you; the deeper and darker the red the closer they are to you. Don't let it go black. Black is the worst possible colour it can go!"  
Nodding, Clara slipped it onto her finger, "What does black mean?"  
"They're within a hundred metres of you." Sighing, the Doctor rested her hands on Clara's shoulders, "I am sorry, I am so sorry Clara. I can't become me again until this stone turns white. I'm so sorry to place this on you." Placing the Chameleon arch on her head, she sighed one last time, "Bollocks."

_Two years later..._

_Dear Diary,_

_The Doctor__ Helena (I really have to refer to her as Helena; because even though she is as stubborn as her- she isn't the doctor. Hell, I still find it a bit weird that she only knows me as Sophie) has been conversing with a strange man named Caturanga. He has taken particular interest in her stories; and her inventive mind. I'm worried he might dig too deeply into her past, the chameleon arch can only compensate for so much. She's gone out with him for lunch today. I tried to join her but she insisted I stay at the house and cover for her. There is something about the man, not that he seems particularly threatening; just he strikes me as a man with a secret.  
I overheard her 'father' talking with Charles earlier; he wants to force her into marriage. Charles seems dead against it; but Mr Wells is adamant. I dread to think what Helena will do.  
Oh well, if the time comes I'm sure she'll find a way to get out of it; she's managed to do so for the last two years. God! Imagine Helena married; or as a mother! I'm not sure if it's a concept I find funny or terrifying._

"Miss Wells... Miss Wells!" Helena turned in shock, acknowledging the older gentleman behind her, "What do you smell?"  
Tilting her head, the young woman considered a moment, "Apples?"


	3. Chapter 3

**Hello! **

**I must apologise for my delay in updating. I was beaten with the essay stick, went home, then the proverbial royally hit the fan. But anyhoo, I shall endeavour to be a more reliable updater. **

**Thank you so much for your fantastic feedback! I hope I don't disappoint. **

_1889_

"NO!" Helena stared incredulously at her brother, "No, Charles! I won't do it!"  
The dark haired man replied solemnly, "Father has already arranged it." Sighing, he shook his head, "Helena, you have brought this on yourself." His voice had a tone of sympathetic frustration, "You disappear for days at a time; I know the Warehouse is important to you but what am I meant to tell father? You're in Egypt... What for? His mind is as sharp as his tongue; he knows something is amiss. Then there are your clothes. You've been caught dressing inappropriately far too often... and the women..."  
Helena's eyes hardened, "Have you...?"  
"No of course not." Charles snapped back, "I wouldn't betray you like that Helena; but you have been too close to discovery for comfort for some time now. Hell, if it wasn't for Sophie, father would have had you institutionalised! You know he is just looking for an excuse to get rid of you!"  
"Charles." Her voice was a low warning.  
Placing his hands on her upper arms, he shook his head, "I just want to protect you. But I need your help." Running a hand through his hair, he took a deep breath, "I will speak with father, but I doubt he will call off the wedding; the arrangements have been made."  
"Helena."  
The young woman felt herself tense as the ever stern voice of her father called her. Turning, she straightened her dress, "Yes father?"  
The sharp featured man held a hand out to his office, "A word."  
Training her features into an unflappable mask she had long since perfected, "Of course."

Clara could hear loud banging from Helena's room. Knocking cautiously she called, "Ma'am?"  
She jumped back as she heard something smash against the door.  
"Ma'am!" Running in, she narrowly avoided a flying book, "Miss Wells, what's wrong?"  
Helena stood shaking in the centre of the room, her face was streaked with angry tears and her jaw was clenched almost to breaking point. "Nothing Sophie. Leave me." Her words her hard and sharp as she spat each one.  
Carefully approaching her, she asked, "What happened?"  
Wiping her eyes with a shaking hand, Helena composed herself, "I have been informed I am to be wed to Mr. Lyons." Her face twisted in disgust.  
"Mr Edward Lyons? I thought you were friends?"  
Her lips turned upwards for the briefest of moments, "Yes, Eddie is a dear friend, but it is not he. I am set to wed his father."  
Clara's jaw dropped in horror, "But he's ancient!"  
Helena's eyes darted up a moment.  
Catching herself, Clara inclined her head, "My apologies Miss, I didn't mean to speak out of turn."  
Sighing, Helena waved the apology away as she sank onto the bed, "It is nothing Sophie, you are right; the man is the same age as father. But since Mrs Lyons' death last year, he has been searching for a new young wife." The woman flinched, "And it would seem I fit the bill." Standing with a sigh, she declared, "I'm going out."

Hurrying through the filthy London streets, Helena felt her heart give a sigh of relief when the small shop that concealed the entrance to the Warehouse came into view. Just as she was about to enter the small puzzle shop, a call came from behind her, "Helena!"  
Turning, her lips twisted into a sad smile, "Eddie, how are you?"  
Tipping his hat, the young man replied, "I have been better. My father just told me about the arrangement; surely you can't be going through with it."  
With a hurt sigh, she shrugged, "What else can I do? The arrangements have been made. The date is set. I have only two weeks!" She gritted her teeth, "I imagine father wanted it to happen as soon as humanly possible in order to limit my window of escape."  
Her friend's face twisted in frustration, "I wish I could..." His eyes brightened, "Helena! Marry me! We'll say we eloped, our parents won't be any the wiser!"  
Pausing, she asked quietly, "But what about...?"  
Glancing to the shop, he seemed nervous, "We'll talk inside."

Turning once within Caturanga's office, she asked, "What about your friend Mr Wallace, Eddie?"  
Resting a hand over hers, his bright blue eyes were honest and imploring, "Helena, Henry would understand. He knows of my affection for you; I cannot abandon you to such a hopeless fate." He worried his lip with his teeth, "Helena, I would not be able to be..." He stammered awkwardly, "As a husband to you. We may have to produce a child in order to satisfy our parents; but I would never..."  
Squeezing his hand, Helena allowed herself to smile. She was in her safe place, "Eddie, I know that. You love Henry, there are no two ways about it!" Taking a moment, she began, "But I couldn't ask it of you."  
It was at that moment Helena's partner McShane walked in, "Lyons, Wells. How are we?"  
The conversation was abruptly halted. Agent McShane was still somewhat of an unknown quantity when it came to such matters, and she preffered to keep it between herself and her apprentice.  
"I am well thank you Mr McShane, and you?"  
Taking off his bowler, he nodded, "I am well."  
"If you will excuse me gentlemen."

Finally comfortable in her trousers and shirt, Helena strolled contentedly through the aisles of Warehouse 12; making notes on the inventory log in her hand.  
Rapid footsteps approached her. Turning, she saw Henry Wallace running towards her, the tails of his tweed jacket whipping out behind him, "HG!"  
"Mr. Wallace."  
Drawing to a halt, he took a moment to catch his breath, "Edward has explained everything to me!" His flushed face was lit up, "We couldn't possibly allow your father to force you into marriage with that beastly man!"  
Stepping back, she returned her eyes to the manifest, "I can't Henry. Aside from your association with Edward, if he were to elope with me, it would destroy his relationship with his father; he risks disownment."  
The smile fell from his face, "Oh... We hadn't..." Shaking away the thought, he insisted, "There must be another way. I am acquainted with his father; the man is a brute. True he is elderly now, but a brute he remains; it is not a character trait that diminishes over time."  
Forcing a lightness into her tone, she tried to shrug good-humouredly, "Then, shall have to pray he dies quickly."

_Dear diary,_

_It's the night before the wedding, and Helena is up-a-height. I can't calm her down for the life of me. I wish this bloody stone would just turn green and be done with it. But the damned thing is still red. The Doctor said that they should be able to survive more than a year. But the colour just pulses. I have a feeling they have to be in the UK, if not within a hundred miles of London; the colour is just too fierce. How can they be so close? There is no way to find us! The Tardis is hidden out in the Kentish countryside for heaven's sake; and the pocket watch is in a safety deposit box in Newcastle. I suppose it is just dumb luck.  
I just hope by some miracle they are gone by morning... then again, the chances of that happening... I wish the Doctor were here; __he __ she'd know what to do. Sometimes I catch myself, there's a glint in her eye; the same spark of genius whenever she is immersed in the technology of the time. God I miss microwaves, and power showers, and pizza, and... God there are so many things I miss. I suppose it could be worse though. London isn't the nicest place; and by that I mean it stinks. The first few weeks were the worst, I suppose I've grown accustomed to it; it's still not pleasant.  
This wedding though... I can't believe her 'father' is making her do this. The bloke, I found out, is actually older than he is! I suppose it's ironic that Helena is actually older than the two of them put together; but it doesn't make it any less horrifying._


End file.
